On the basis of the structure of DNA-psoralen bis adducts (formed by psoralen with two thymines on opposite strands), a psoralen-oligonucleotide conjugate was designed to photoinduce a cross-link between the two DNA strands at a specific sequence. Psoralen was attached via its C-5 position to a 5'-thiophosphate group of an 11-mer homopyrimidine oligonucleotide. The 11-mer binds to an 11-base-pair homopurinehomopyrimidine sequence of a DNA fragment, where it forms a triple helix. Upon near-UV-irradiation, the two strands of DNA are crosslinked at the TpA step present at the triplex-duplex junction. The reaction is specific for the homopurine'homopyrimidine DNA sequence and requires both oligonucleotide recognition of the DNA major groove and intercalation of psoralen at the triplex-duplex junction. The yield of the photoinduced cross-linking reaction is quite high (>80%). Such psoralen-oligonucleotide conjugates are probes of sequencespecific triple-helix formation and could be used to selectively control gene expression or to induce site-directed mutations.
The guanine‐specific cleavage of oligonucleotides is achieved with the conjugate 1, which contains a fullerene tethered to a tetradecadeoxyribonucleotide Nu(pNu)n. This conjugate was able to form a duplex with a complementary oligonucleotide, and triplexes with appropriate double‐stranded oligonucleotides. Irradiation of the complexes leads to site‐specfic cleavage of the target sequences—probably through the action of singlet oxygen.
Conjugates of oligonucleotides with chlorin-type photosensitizers
were prepared. Two chlorin moieties,
CPP and CHEVP, characterized by a modified pyrrole unit bearing an
aldehyde chain, were photochemically prepared
from protoporphyrin and heptaethylvinylporphyrin, respectively.
These chlorin moieties were coupled through the
carboxylic acid side-chain (CPP) or aldehyde side-chain (CHEVP) to the
3‘-activated phosphate of oligodeoxynucleotides. Diamine or dihydrazide were used as linkers. The
resulting conjugates were purified by HPLC and
characterized by electrophoresis, UV−visible spectroscopy, and mass
spectrometry. The photosensitizing properties
of the conjugate of CHEVP with the 14-mer oligodeoxynucleotide
TTCTTCTCCTTTCT were investigated using
three different targets. A single-stranded 25-mer containing the
complementary sequence of the 14-mer formed a
double helix with the chlorin-14-mer conjugate. A 24 base-pair
duplex and a 41-mer hairpin with 18 base pairs and
a five nucleotide loop formed triple helices with the conjugate.
In all cases, upon irradiation with visible light
(428
or 668 nm), piperidine-labile sites at guanine positions were produced.
The reaction required oxygen and was inhibited
to some extent by sodium azide. The cleavage sites were correlated
with the chlorin position in both the duplex and
triplex structures. In the 41-mer hairpin, the most reactive
guanines were those located in the loop region. The
quantum yield for cleavage of the hairpin structure was determined to
be about 10-3, independent of the
excitation
wavelength. This modest value is largely compensated by the high
absorption of the chlorin in the red, making the
conjugate highly efficient even under low light fluence. No effect
was found with a noncomplementary chlorin-oligonucleotide conjugate. These results show that site-directed
damages to nucleic acid structures can be achieved
using oligonucleotide-chlorin conjugates and red light
irradiation.
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